02623nas a2200217   4500000000100000008004100001653003500042653002500077653001200102653003100114653002400145100001500169700001500184700001400199245015000213856007900363300000700442490000600449520193600455022001402391       2016                            d10aProtein–protein interactions10aMycobacterium leprae10aleprosy10aGenome reductive evolution10aFunctional analysis1 aAkinola RO1 aMazandu GK1 aMulder NJ00aA Quantitative Approach to Analyzing Genome Reductive Evolution Using Protein-Protein Interaction Networks: A Case Study of Mycobacterium leprae.  uhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC4809885/pdf/fgene-07-00039.pdf  a390 v73 a<p>The advance in high-throughput sequencing technologies has yielded complete genome sequences of several organisms, including complete bacterial genomes. The growing number of these available sequenced genomes has enabled analyses of their dynamics, as well as the molecular and evolutionary processes which these organisms are under. Comparative genomics of different bacterial genomes have highlighted their genome size and gene content in association with lifestyles and adaptation to various environments and have contributed to enhancing our understanding of the mechanisms of their evolution. Protein-protein functional interactions mediate many essential processes for maintaining the stability of the biological systems under changing environmental conditions. Thus, these interactions play crucial roles in the evolutionary processes of different organisms, especially for obligate intracellular bacteria, proven to generally have reduced genome sizes compared to their nearest free-living relatives. In this study, we used the approach based on the Renormalization Group (RG) analysis technique and the Maximum-Excluded-Mass-Burning (MEMB) model to investigate the evolutionary process of genome reduction in relation to the organization of functional networks of two organisms. Using a Mycobacterium leprae (MLP) network in comparison with a Mycobacterium tuberculosis (MTB) network as a case study, we show that reductive evolution in MLP was as a result of removal of important proteins from neighbors of corresponding orthologous MTB proteins. While each orthologous MTB protein had an increase in number of interacting partners in most instances, the corresponding MLP protein had lost some of them. This work provides a quantitative model for mapping reductive evolution and protein-protein functional interaction network organization in terms of roles played by different proteins in the network structure.</p>
  a1664-8021